// StateRemover.java
//
// (c) 1999-2001 PAL Development Core Team
//
// This package may be distributed under the
// terms of the Lesser GNU General Public License (LGPL)

package pal.datatype;

/** A standard data type, but with characters removed */
public class StateRemover extends SimpleDataType implements java.io.Serializable {
	DataType toAdjust_;

  int[] originalToAdjusted_; /** A translation array -> originalToAdjusted_["original State"] = "adjusted state" */
  int[] adjustedToOriginal_; /** A translation array -> originalToAdjusted_["adjusted State"] = "original state" */

  public StateRemover(DataType toAdjust, int[] statesToRemove) {
    this.toAdjust_ = toAdjust;
  	createTranslationTables(toAdjust.getNumStates(),statesToRemove);
  }

  private final void createTranslationTables(int numberOfOriginalStates, int[] statesToRemove) {
  	originalToAdjusted_ = new int[numberOfOriginalStates];
		adjustedToOriginal_ = new int[numberOfOriginalStates-statesToRemove.length];
    int currentAdjustedState = 0;
    for(int i = 0 ; i < numberOfOriginalStates ; i++ ) {
    	boolean removeState = false;
    	for(int j = 0 ; j < statesToRemove.length ; j++) {
      	if(statesToRemove[j] == i) {
        	removeState = true;
        	break;
        }
			}
			if(removeState) {
				originalToAdjusted_[i] = adjustedToOriginal_.length;
			} else {
				originalToAdjusted_[i] = currentAdjustedState;
				adjustedToOriginal_[currentAdjustedState] = i;
				currentAdjustedState++;
      }
    }
  }

	// Get number of bases
	public int getNumStates()	{
		return adjustedToOriginal_.length;
	}

	/**
		* @retrun true if this state is an unknown state
		*/
	public boolean isUnknownState(int state) {
		return(state>=adjustedToOriginal_.length);
	}


	public int getState(char c)	{
  	int unadjustedState = toAdjust_.getState(c);
  	if(!toAdjust_.isUnknownState(unadjustedState)) {
			return originalToAdjusted_[unadjustedState]; /* May also return unknown, see constructor*/
		}
		return adjustedToOriginal_.length;
	}

	/**
	 * Get character corresponding to a given state
 	 */
	public char getChar(int state)
	{
  	if(state>adjustedToOriginal_.length) {
     	return UNKNOWN_CHARACTER;
    }
  	return toAdjust_.getChar(adjustedToOriginal_[state]);
	}

	// String describing the data type
	public String getDescription()
	{
		return toAdjust_.getDescription()+" with states removed";
	}

	// Get numerical code describing the data type
	public int getTypeID()
	{
		return toAdjust_.getTypeID();
	}



}

